The goal of this research project is to use the principles of hierarchically organized self-assembly to design a multiplexed sequence specific DNA detection strategy based on semiconductor quantum dots (QDs) with applications in genomic analysis. Water-soluble and stable semiconductor QDs will be selected, synthesized and modified to be used as a substitute for conventional fluorophores. Furthermore, procedures to efficiently attach different oligonucleotide recognition elements capable of selective binding to specific targets will be tested. An array of various types of QDs will be evaluated as a detection system, based on their ability to utilize the molecular recognition properties of the oligonucleotides to participate in a self-assembly process that can visualized via changes in spectroscopic characteristics of the QDs. The results of these proof-of concept studies can be used the implementation of truly interdisciplinary approaches to the analysis of genomic information.